molstar
Version:
A comprehensive macromolecular library.
303 lines (302 loc) • 17.6 kB
JavaScript
/**
* Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Gianluca Tomasello <giagitom@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { Unit } from '../../../mol-model/structure';
import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
import { Segmentation } from '../../../mol-data/int';
import { isNucleic } from '../../../mol-model/structure/model/types';
import { addCylinder } from '../../../mol-geo/geometry/mesh/builder/cylinder';
import { UnitsMeshParams, UnitsMeshVisual, UnitsCylindersParams, UnitsCylindersVisual } from '../units-visual';
import { NucleotideLocationIterator, getNucleotideElementLoci, eachNucleotideElement, getNucleotideBaseType, createNucleicIndices, setSugarIndices, hasSugarIndices, setPurinIndices, hasPurinIndices, setPyrimidineIndices, hasPyrimidineIndices } from './util/nucleotide';
import { BaseGeometry } from '../../../mol-geo/geometry/base';
import { Sphere3D } from '../../../mol-math/geometry';
import { Cylinders } from '../../../mol-geo/geometry/cylinders/cylinders';
import { CylindersBuilder } from '../../../mol-geo/geometry/cylinders/cylinders-builder';
const pTrace = Vec3();
const pN1 = Vec3();
const pC2 = Vec3();
const pN3 = Vec3();
const pC4 = Vec3();
const pC5 = Vec3();
const pC6 = Vec3();
const pN7 = Vec3();
const pC8 = Vec3();
const pN9 = Vec3();
const pC1_1 = Vec3();
const pC2_1 = Vec3();
const pC3_1 = Vec3();
const pC4_1 = Vec3();
const pO4_1 = Vec3();
export const NucleotideAtomicBondParams = {
...UnitsMeshParams,
...UnitsCylindersParams,
sizeFactor: PD.Numeric(0.3, { min: 0, max: 10, step: 0.01 }),
radialSegments: PD.Numeric(16, { min: 2, max: 56, step: 2 }, BaseGeometry.CustomQualityParamInfo),
tryUseImpostor: PD.Boolean(true)
};
export function NucleotideAtomicBondVisual(materialId, structure, props, webgl) {
return props.tryUseImpostor && webgl && webgl.extensions.fragDepth
? NucleotideAtomicBondImpostorVisual(materialId)
: NucleotideAtomicBondMeshVisual(materialId);
}
function createNucleotideAtomicBondImpostor(ctx, unit, structure, theme, props, cylinders) {
if (!Unit.isAtomic(unit))
return Cylinders.createEmpty(cylinders);
const nucleotideElementCount = unit.nucleotideElements.length;
if (!nucleotideElementCount)
return Cylinders.createEmpty(cylinders);
const cylindersCountEstimate = nucleotideElementCount * 15; // 15 is the average purine (17) & pirimidine (13) bonds
const builder = CylindersBuilder.create(cylindersCountEstimate, cylindersCountEstimate / 4, cylinders);
const { elements, model, conformation: c } = unit;
const { chainAtomSegments, residueAtomSegments } = model.atomicHierarchy;
const { moleculeType } = model.atomicHierarchy.derived.residue;
const chainIt = Segmentation.transientSegments(chainAtomSegments, elements);
const residueIt = Segmentation.transientSegments(residueAtomSegments, elements);
let i = 0;
const colorModeFlag = 2.0;
while (chainIt.hasNext) {
residueIt.setSegment(chainIt.move());
while (residueIt.hasNext) {
const { index: residueIndex } = residueIt.move();
if (isNucleic(moleculeType[residueIndex])) {
const idx = createNucleicIndices();
setSugarIndices(idx, unit, residueIndex);
if (hasSugarIndices(idx)) {
c.invariantPosition(idx.C1_1, pC1_1);
c.invariantPosition(idx.C2_1, pC2_1);
c.invariantPosition(idx.C3_1, pC3_1);
c.invariantPosition(idx.C4_1, pC4_1);
c.invariantPosition(idx.O4_1, pO4_1);
// trace cylinder
c.invariantPosition(idx.trace, pTrace);
builder.add(pC3_1[0], pC3_1[1], pC3_1[2], pTrace[0], pTrace[1], pTrace[2], 1, true, true, colorModeFlag, i);
// sugar ring
builder.add(pC3_1[0], pC3_1[1], pC3_1[2], pC4_1[0], pC4_1[1], pC4_1[2], 1, true, true, colorModeFlag, i);
builder.add(pC4_1[0], pC4_1[1], pC4_1[2], pO4_1[0], pO4_1[1], pO4_1[2], 1, true, true, colorModeFlag, i);
builder.add(pO4_1[0], pO4_1[1], pO4_1[2], pC1_1[0], pC1_1[1], pC1_1[2], 1, true, true, colorModeFlag, i);
builder.add(pC1_1[0], pC1_1[1], pC1_1[2], pC2_1[0], pC2_1[1], pC2_1[2], 1, true, true, colorModeFlag, i);
builder.add(pC2_1[0], pC2_1[1], pC2_1[2], pC3_1[0], pC3_1[1], pC3_1[2], 1, true, true, colorModeFlag, i);
}
const { isPurine, isPyrimidine } = getNucleotideBaseType(unit, residueIndex);
if (isPurine) {
setPurinIndices(idx, unit, residueIndex);
if (idx.C1_1 !== -1 && idx.N9 !== -1) {
c.invariantPosition(idx.C1_1, pC1_1);
c.invariantPosition(idx.N9, pN9);
builder.add(pN9[0], pN9[1], pN9[2], pC1_1[0], pC1_1[1], pC1_1[2], 1, true, true, colorModeFlag, i);
}
else if (idx.N9 !== -1 && idx.trace !== -1) {
c.invariantPosition(idx.N9, pN9);
c.invariantPosition(idx.trace, pTrace);
builder.add(pN9[0], pN9[1], pN9[2], pTrace[0], pTrace[1], pTrace[2], 1, true, true, colorModeFlag, i);
}
if (hasPurinIndices(idx)) {
c.invariantPosition(idx.N1, pN1);
c.invariantPosition(idx.C2, pC2);
c.invariantPosition(idx.N3, pN3);
c.invariantPosition(idx.C4, pC4);
c.invariantPosition(idx.C5, pC5);
c.invariantPosition(idx.C6, pC6);
c.invariantPosition(idx.N7, pN7);
c.invariantPosition(idx.C8, pC8);
c.invariantPosition(idx.N9, pN9);
// base ring
builder.add(pN9[0], pN9[1], pN9[2], pC8[0], pC8[1], pC8[2], 1, true, true, colorModeFlag, i);
builder.add(pC8[0], pC8[1], pC8[2], pN7[0], pN7[1], pN7[2], 1, true, true, colorModeFlag, i);
builder.add(pN7[0], pN7[1], pN7[2], pC5[0], pC5[1], pC5[2], 1, true, true, colorModeFlag, i);
builder.add(pC5[0], pC5[1], pC5[2], pC6[0], pC6[1], pC6[2], 1, true, true, colorModeFlag, i);
builder.add(pC6[0], pC6[1], pC6[2], pN1[0], pN1[1], pN1[2], 1, true, true, colorModeFlag, i);
builder.add(pN1[0], pN1[1], pN1[2], pC2[0], pC2[1], pC2[2], 1, true, true, colorModeFlag, i);
builder.add(pC2[0], pC2[1], pC2[2], pN3[0], pN3[1], pN3[2], 1, true, true, colorModeFlag, i);
builder.add(pN3[0], pN3[1], pN3[2], pC4[0], pC4[1], pC4[2], 1, true, true, colorModeFlag, i);
builder.add(pC4[0], pC4[1], pC4[2], pC5[0], pC5[1], pC5[2], 1, true, true, colorModeFlag, i);
builder.add(pC4[0], pC4[1], pC4[2], pN9[0], pN9[1], pN9[2], 1, true, true, colorModeFlag, i);
}
}
else if (isPyrimidine) {
setPyrimidineIndices(idx, unit, residueIndex);
if (idx.C1_1 !== -1 && idx.N1 !== -1) {
c.invariantPosition(idx.N1, pN1);
c.invariantPosition(idx.C1_1, pC1_1);
builder.add(pN1[0], pN1[1], pN1[2], pC1_1[0], pC1_1[1], pC1_1[2], 1, true, true, colorModeFlag, i);
}
else if (idx.N1 !== -1 && idx.trace !== -1) {
c.invariantPosition(idx.N1, pN1);
c.invariantPosition(idx.trace, pTrace);
builder.add(pN1[0], pN1[1], pN1[2], pTrace[0], pTrace[1], pTrace[2], 1, true, true, colorModeFlag, i);
}
if (hasPyrimidineIndices(idx)) {
c.invariantPosition(idx.N1, pN1);
c.invariantPosition(idx.C2, pC2);
c.invariantPosition(idx.N3, pN3);
c.invariantPosition(idx.C4, pC4);
c.invariantPosition(idx.C5, pC5);
c.invariantPosition(idx.C6, pC6);
// base ring
builder.add(pN1[0], pN1[1], pN1[2], pC6[0], pC6[1], pC6[2], 1, true, true, colorModeFlag, i);
builder.add(pC6[0], pC6[1], pC6[2], pC5[0], pC5[1], pC5[2], 1, true, true, colorModeFlag, i);
builder.add(pC5[0], pC5[1], pC5[2], pC4[0], pC4[1], pC4[2], 1, true, true, colorModeFlag, i);
builder.add(pC4[0], pC4[1], pC4[2], pN3[0], pN3[1], pN3[2], 1, true, true, colorModeFlag, i);
builder.add(pN3[0], pN3[1], pN3[2], pC2[0], pC2[1], pC2[2], 1, true, true, colorModeFlag, i);
builder.add(pC2[0], pC2[1], pC2[2], pN1[0], pN1[1], pN1[2], 1, true, true, colorModeFlag, i);
}
}
++i;
}
}
}
const cy = builder.getCylinders();
const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
cy.setBoundingSphere(sphere);
return cy;
}
export function NucleotideAtomicBondImpostorVisual(materialId) {
return UnitsCylindersVisual({
defaultProps: PD.getDefaultValues(NucleotideAtomicBondParams),
createGeometry: createNucleotideAtomicBondImpostor,
createLocationIterator: NucleotideLocationIterator.fromGroup,
getLoci: getNucleotideElementLoci,
eachLocation: eachNucleotideElement,
setUpdateState: (state, newProps, currentProps) => {
state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor);
},
mustRecreate: (structureGroup, props, webgl) => {
return !props.tryUseImpostor || !webgl;
}
}, materialId);
}
function createNucleotideAtomicBondMesh(ctx, unit, structure, theme, props, mesh) {
if (!Unit.isAtomic(unit))
return Mesh.createEmpty(mesh);
const nucleotideElementCount = unit.nucleotideElements.length;
if (!nucleotideElementCount)
return Mesh.createEmpty(mesh);
const { sizeFactor, radialSegments } = props;
const vertexCount = nucleotideElementCount * (radialSegments * 15); // 15 is the average purine (17) & pirimidine (13) bonds
const builderState = MeshBuilder.createState(vertexCount, vertexCount / 4, mesh);
const { elements, model, conformation: c } = unit;
const { chainAtomSegments, residueAtomSegments } = model.atomicHierarchy;
const { moleculeType } = model.atomicHierarchy.derived.residue;
const chainIt = Segmentation.transientSegments(chainAtomSegments, elements);
const residueIt = Segmentation.transientSegments(residueAtomSegments, elements);
const cylinderProps = { radiusTop: 1 * sizeFactor, radiusBottom: 1 * sizeFactor, radialSegments };
let i = 0;
while (chainIt.hasNext) {
residueIt.setSegment(chainIt.move());
while (residueIt.hasNext) {
const { index: residueIndex } = residueIt.move();
if (isNucleic(moleculeType[residueIndex])) {
const idx = createNucleicIndices();
builderState.currentGroup = i;
setSugarIndices(idx, unit, residueIndex);
if (hasSugarIndices(idx)) {
c.invariantPosition(idx.C1_1, pC1_1);
c.invariantPosition(idx.C2_1, pC2_1);
c.invariantPosition(idx.C3_1, pC3_1);
c.invariantPosition(idx.C4_1, pC4_1);
c.invariantPosition(idx.O4_1, pO4_1);
// trace cylinder
c.invariantPosition(idx.trace, pTrace);
addCylinder(builderState, pC3_1, pTrace, 1, cylinderProps);
// sugar ring
addCylinder(builderState, pC3_1, pC4_1, 1, cylinderProps);
addCylinder(builderState, pC4_1, pO4_1, 1, cylinderProps);
addCylinder(builderState, pO4_1, pC1_1, 1, cylinderProps);
addCylinder(builderState, pC1_1, pC2_1, 1, cylinderProps);
addCylinder(builderState, pC2_1, pC3_1, 1, cylinderProps);
}
const { isPurine, isPyrimidine } = getNucleotideBaseType(unit, residueIndex);
if (isPurine) {
setPurinIndices(idx, unit, residueIndex);
if (idx.C1_1 !== -1 && idx.N9 !== -1) {
c.invariantPosition(idx.C1_1, pC1_1);
c.invariantPosition(idx.N9, pN9);
addCylinder(builderState, pN9, pC1_1, 1, cylinderProps);
}
else if (idx.N9 !== -1 && idx.trace !== -1) {
c.invariantPosition(idx.N9, pN9);
c.invariantPosition(idx.trace, pTrace);
addCylinder(builderState, pN9, pTrace, 1, cylinderProps);
}
if (hasPurinIndices(idx)) {
c.invariantPosition(idx.N1, pN1);
c.invariantPosition(idx.C2, pC2);
c.invariantPosition(idx.N3, pN3);
c.invariantPosition(idx.C4, pC4);
c.invariantPosition(idx.C5, pC5);
c.invariantPosition(idx.C6, pC6);
c.invariantPosition(idx.N7, pN7);
c.invariantPosition(idx.C8, pC8);
c.invariantPosition(idx.N9, pN9);
// base ring
addCylinder(builderState, pN9, pC8, 1, cylinderProps);
addCylinder(builderState, pC8, pN7, 1, cylinderProps);
addCylinder(builderState, pN7, pC5, 1, cylinderProps);
addCylinder(builderState, pC5, pC6, 1, cylinderProps);
addCylinder(builderState, pC6, pN1, 1, cylinderProps);
addCylinder(builderState, pN1, pC2, 1, cylinderProps);
addCylinder(builderState, pC2, pN3, 1, cylinderProps);
addCylinder(builderState, pN3, pC4, 1, cylinderProps);
addCylinder(builderState, pC4, pC5, 1, cylinderProps);
addCylinder(builderState, pC4, pN9, 1, cylinderProps);
}
}
else if (isPyrimidine) {
setPyrimidineIndices(idx, unit, residueIndex);
if (idx.C1_1 !== -1 && idx.N1 !== -1) {
c.invariantPosition(idx.N1, pN1);
c.invariantPosition(idx.C1_1, pC1_1);
addCylinder(builderState, pN1, pC1_1, 1, cylinderProps);
}
else if (idx.N1 !== -1 && idx.trace !== -1) {
c.invariantPosition(idx.N1, pN1);
c.invariantPosition(idx.trace, pTrace);
addCylinder(builderState, pN1, pTrace, 1, cylinderProps);
}
if (hasPyrimidineIndices(idx)) {
c.invariantPosition(idx.N1, pN1);
c.invariantPosition(idx.C2, pC2);
c.invariantPosition(idx.N3, pN3);
c.invariantPosition(idx.C4, pC4);
c.invariantPosition(idx.C5, pC5);
c.invariantPosition(idx.C6, pC6);
// base ring
addCylinder(builderState, pN1, pC6, 1, cylinderProps);
addCylinder(builderState, pC6, pC5, 1, cylinderProps);
addCylinder(builderState, pC5, pC4, 1, cylinderProps);
addCylinder(builderState, pC4, pN3, 1, cylinderProps);
addCylinder(builderState, pN3, pC2, 1, cylinderProps);
addCylinder(builderState, pC2, pN1, 1, cylinderProps);
}
}
++i;
}
}
}
const m = MeshBuilder.getMesh(builderState);
const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
m.setBoundingSphere(sphere);
return m;
}
export function NucleotideAtomicBondMeshVisual(materialId) {
return UnitsMeshVisual({
defaultProps: PD.getDefaultValues(NucleotideAtomicBondParams),
createGeometry: createNucleotideAtomicBondMesh,
createLocationIterator: NucleotideLocationIterator.fromGroup,
getLoci: getNucleotideElementLoci,
eachLocation: eachNucleotideElement,
setUpdateState: (state, newProps, currentProps) => {
state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.radialSegments !== currentProps.radialSegments);
},
mustRecreate: (structureGroup, props, webgl) => {
return props.tryUseImpostor && !!webgl;
}
}, materialId);
}